R Notebook

library(monocle)
library(cowplot)

Monocle per depot

3 feature selection methods: 1) Same feature selection strategy as for the whole dataset (split each depot into T1T2T3 and T4T5, cluster, perform DE tests on clusters, take union of resulting gene lists as features); 2) Genes with high dispersion; 3) Genes used for computing the trajectory of the whole dataset.

cds_peri <- readRDS('output/monocle/180831/peri/monocle_peri_T1T2T3_T4T5_res1/10x-180831-peri-monocle')
cds_peri_disp <- readRDS('output/monocle/180831/peri/monocle_peri_high-dispersion/10x-180831-peri-monocle')
cds_peri_gl <- readRDS('output/monocle/180831/peri/monocle_peri_genelist/10x-180831-peri-monocle')

plot_grid(
  plot_cell_trajectory(cds_peri, color_by='timepoint'),
  plot_cell_trajectory(cds_peri_disp, color_by='timepoint'),
  plot_cell_trajectory(cds_peri_gl, color_by='timepoint'),
  plot_cell_trajectory(cds_peri, color_by='State.old') + scale_color_manual(values=c("#f67770", "#964B00", "orange"), name = "State"),
  plot_cell_trajectory(cds_peri_disp, color_by='State.old') + scale_color_manual(values=c("#f67770", "#964B00", "orange"), name = "State"),
  plot_cell_trajectory(cds_peri_gl, color_by='State.old') + scale_color_manual(values=c("#f67770", "#964B00", "orange"), name = "State"),
  ncol=3
)

cds_supra <- readRDS('output/monocle/180831/supra/monocle_supra_T1T2T3_T4T5_res1/10x-180831-supra-monocle')
cds_supra_disp <- readRDS('output/monocle/180831/supra/monocle_supra_high-dispersion/10x-180831-supra-monocle')
cds_supra_gl <- readRDS('output/monocle/180831/supra/monocle_supra_genelist/10x-180831-supra-monocle')

plot_grid(
  plot_cell_trajectory(cds_supra, color_by='timepoint'),
  plot_cell_trajectory(cds_supra_disp, color_by='timepoint'),
  plot_cell_trajectory(cds_supra_gl, color_by='timepoint'),
  plot_cell_trajectory(cds_supra, color_by='State.old') + scale_color_manual(values=c("#f67770", "#964B00", "orange"), name = "State"),
  plot_cell_trajectory(cds_supra_disp, color_by='State.old') + scale_color_manual(values=c("#f67770", "#964B00", "orange"), name = "State"),
  plot_cell_trajectory(cds_supra_gl, color_by='State.old') + scale_color_manual(values=c("#f67770", "#964B00", "orange"), name = "State"),
  ncol=3
)

cds_subq <- readRDS('output/monocle/180831/subq/monocle_subq_T1T2T3_T4T5_res1/10x-180831-subq-monocle')
cds_subq_disp <- readRDS('output/monocle/180831/subq/monocle_subq_high-dispersion/10x-180831-subq-monocle')
cds_subq_gl <- readRDS('output/monocle/180831/subq/monocle_subq_genelist/10x-180831-subq-monocle')

plot_grid(
  plot_cell_trajectory(cds_subq, color_by='timepoint'),
  plot_cell_trajectory(cds_subq_disp, color_by='timepoint'),
  plot_cell_trajectory(cds_subq_gl, color_by='timepoint'),
  plot_cell_trajectory(cds_subq, color_by='State.old') + scale_color_manual(values=c("#f67770", "#964B00", "orange"), name = "State"),
  plot_cell_trajectory(cds_subq_disp, color_by='State.old') + scale_color_manual(values=c("#f67770", "#964B00", "orange"), name = "State"),
  plot_cell_trajectory(cds_subq_gl, color_by='State.old') + scale_color_manual(values=c("#f67770", "#964B00", "orange"), name = "State"),
  ncol=3
)

cds_visce <- readRDS('output/monocle/180831/visce/monocle_visce_T1T2T3_T4T5_res1/10x-180831-visce-monocle')
cds_visce_disp <- readRDS('output/monocle/180831/visce/monocle_visce_high-dispersion/10x-180831-visce-monocle')
cds_visce_gl <- readRDS('output/monocle/180831/visce/monocle_visce_genelist/10x-180831-visce-monocle')

plot_grid(
  plot_cell_trajectory(cds_visce, color_by='timepoint'),
  plot_cell_trajectory(cds_visce_disp, color_by='timepoint'),
  plot_cell_trajectory(cds_visce_gl, color_by='timepoint'),
  plot_cell_trajectory(cds_visce, color_by='State.old') + scale_color_manual(values=c("#f67770", "#964B00", "orange"), name = "State"),
  plot_cell_trajectory(cds_visce_disp, color_by='State.old') + scale_color_manual(values=c("#f67770", "#964B00", "orange"), name = "State"),
  plot_cell_trajectory(cds_visce_gl, color_by='State.old') + scale_color_manual(values=c("#f67770", "#964B00", "orange"), name = "State"),
  ncol=3
)

plot_grid(
  plot_cell_trajectory(cds_peri, color_by='State.old') + scale_color_manual(values=c("#f67770", "#964B00", "orange"), name = "State"),
  plot_cell_trajectory(cds_supra, color_by='State.old') + scale_color_manual(values=c("#f67770", "#964B00", "orange"), name = "State"),
  plot_cell_trajectory(cds_subq, color_by='State.old') + scale_color_manual(values=c("#f67770", "#964B00", "orange"), name = "State"),
  plot_cell_trajectory(cds_visce, color_by='State.old') + scale_color_manual(values=c("#f67770", "#964B00", "orange"), name = "State"),
  ncol=2
)

plot_grid(
  plot_cell_trajectory(cds_peri, color_by='State'),
  plot_cell_trajectory(cds_supra, color_by='State'), 
  plot_cell_trajectory(cds_subq, color_by='State'), 
  plot_cell_trajectory(cds_visce, color_by='State'),
  ncol=2
)